The overall goal of this proposal is to develop a quantitative understanding of how prior immunity affects the dynamics and evolution of recall immune responses to viruses. This requires developing mathematical models for the dynamics of virus and immunity following immunization and infection and validating the models experimentally. We choose the influenza system because of tractability (the ability to modulate the antigenic properties of the virus and measure the immune responses in model infections of mice), access to samples following immunization or infection of humans, and its direct relevance to human health. We have assembled a multi-disciplinary team with expertise in both theory and experimental studies in mice and humans influenza. The PI's of this multi-PI proposal Rustom Antia and Rafi Ahmed are long-term collaborators with experience in integrating modeling with experimental data in immunology. The team includes: Joshy Jacob (B & T cell responses to influenza), Brian Evavold & Veronika Zarnitsyna (T cell responses /affinity/diversity), Jacob Kohlmeier (resident memory T cells/influenza), Anice Lowen and John Steel (influenza virus engineering) at Emory University joined by Andreas Handel (UGA: modeling/statistics/T cell diversity/influenza); Paul Thomas (St. Judes: influenza in mice/humans), and Trevor Bedford and Erick Matsen (FHCRC: phylodynamics/statistics). In Project 1 Aim 1 we will develop models for the dynamics of humoral responses following immunization. In Aim 2 we model CD8 T cell responses to influenza viruses with focus on resident memory CD8 T cells in the lungs. Aim 3 combines models from Aim 1, 2 to generate a predictive model for how pre-existing immunity to influenza affects the dynamics of virus and immunity following challenge with new strains. We will use phylodynamics approach to infer the dynamics of B and T cell clones competition from sequencing virus- specific B and T cells. Aim 4 is devoted to the development and dissemination of user-friendly modeling tools that can be used by the wider research community for immunological modeling. In Project 2 Aims 1-3 we will validate our models from the corresponding Aims 1-3 of Project 1 in the mouse system by following the immune responses to reverse genetics-derived influenza viruses with modified B and T cell epitopes and recombinant hemagglutinin (HA) protein as viral antigens. This will lead to further model development in Project 1. Finally, in Aim 4 of Project 2 we will test the consistency of our verified and refined n mouse system models using humans samples banked from studies on vaccination with trivalent influenza vaccines and natural influenza infection. The validated models we develop will lay the foundation to explore different strategies for improving vaccination to influenza and other pathogens.